This paper investigates secondary winding structures in a multi-core transformer in a MHz inverter using a frequency multiplying method at the output frequency of 2.5 MHz which is five times of the switching frequency of 500 kHz. The proposed circuit can generate high output frequency by using a multi-phase inverter with phase shift control and the multi-core transformer while the switching frequency and an operational frequency of the multi-core transformer is lower than the output frequency. Therefore, an iron loss of the multi-core transformer is reduced, which results in high efficiency. In this paper, two prototypes of the multi-core transformers which have different secondary winding structures are made and compared from the view point of a leakage inductance and a parasitic capacitance viewed from the secondary side of the multi-core transformer. As a result, it is confirmed that the effect of the parasitic capacitance viewed from the secondary side of the multi-core transformer to a series resonant capacitor connected to the secondary side of the multi-core transformer in series is reduced to 1/4 compared with a loosely-coupled multi-core transformer by a highly-coupled multi-core transformer.